Editorial pubs.acs.org/jmc
Digital Chemistry in the Journal of Medicinal Chemistry s arguably the central journal in its field, the Journal of Medicinal Chemistry is a treasure trove of medicinal chemistry information. This information is still provided in a traditional print format, optimized over many years to be compact and yet easily understood by readers. Today, however, few readers have print subscriptions to the journal, and those of us with Web subscriptions rarely print out our electronic articles. Instead, we view them on computers and tablets, and these new media are creating exciting opportunities to innovate and enhance the value of our articles to readers. In addition, we are all benefiting from a Web of chemogenomics, systems biology, bioinformatics, and other Internet-based information resources that have sprung up in recent years. The value of the Journal of Medicinal Chemistry will be greatly enhanced if the data it contains can be thoughtfully integrated into this online data ecosystem. With this issue, therefore, the Journal of Medicinal Chemistry embarks on an initiative to integrate the chemical information it publishes with digital media and chemical software. The first step in this effort is the linkage of articles with molecular formulas in a format that can be generated by and read into chemical software. The immediate benefit is that readers will be able to transfer compounds from articles into chemical drawing programs, databases, and computational tools. In the near future, this association of articles with computer-readable chemical formulas will provide a foundation for the creation of new journal features that will bring chemistry to life on the Web and in digital readers and tablets. Authors are invited to use their existing chemical drawing programs (e.g., ChemDraw, ACD ChemSketch, Marvin Sketch) to generate a computer-readable SMILES formula1 for each compound presented in their articles. These formulas are then pasted into a simple spreadsheet, along with basic information about each compound. Ideally, this spreadsheet will provide a machine-readable version of the key data presented in the article’s tables. This approach, which balances functionality with ease of implementation and use, was developed by a committee comprising researchers and editors of the Journal of Medicinal Chemistry (Michael Gilson, Michael A. Walters, Patrick Walters, Carrie Haskell-Luevano, Gunda Georg, and Shaomeng Wang) and members of the ACS Publications Division and CAS (Janice Silverman and Kathy Wolfgram) in consultation with other individuals. It is worth noting that although InChi2 molecular formulas were seriously considered, the SMILES format was selected because its conventions allow it to preserve the author’s chemical drawings more faithfully. Incorporating computer-readable molecular formulas into Journal of Medicinal Chemistry articles is a simple yet powerful step toward making the journal even more relevant and useful in this digital age. Because the molecular formula spreadsheet makes the chemical information in an article so much more accessible, we expect it to raise the profile of articles that include it, and we hope that authors will find the process of filling out the molecular formula spreadsheet to be straightforward and worthwhile. In the coming year, we will work closely
A
© 2014 American Chemical Society
with ACS Publications staff to monitor the progress of this new initiative. We recognize that adjustments may be warranted and invite your comments and suggestions. Please send your comments to [email protected]. This issue’s Featured Article breaks ground for the Journal, as it is the first ever to include the new spreadsheet. All prospective authors are encouraged to follow suit, and all readers are invited to make use of the new data files. We hope that this initiative will stimulate other journals in the field to link their articles too, with compounds identifiers in the computer-readable SMILES format. This bridge between the written word and digital science has the potential to become a powerful tool in medicinal chemistry, chemical biology, and drug discovery.
Michael K. Gilson, Chair Molecular String Committee on Behalf of Journal of Medicinal Chemistry
Gunda Georg, Editor Journal of Medicinal Chemistry
Shaomeng Wang, Editor
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Journal of Medicinal Chemistry
AUTHOR INFORMATION
Notes
The views expressed in this editorial are those of the author and not necessarily the views of the ACS.
■
REFERENCES
(1) Weininger, D. SMILES, a Chemical Language and InformationSystem. 1. Introduction to Methodology and Encoding Rules. J. Chem. Inf. Comput. Sci. 1988, 28, 31−36. (2) Stein, S. E.; Heller, S. R.; Tchekhovski, D. An Open Standard for Chemical Structure RepresentationThe IUPAC Chemical Identifier. Nimes Int. Chem. Inf. Conf. Proc. 2003, 143.
Published: February 12, 2014 1137
dx.doi.org/10.1021/jm5002056 | J. Med. Chem. 2014, 57, 1137−1137
Digital Chemistry in the Journal of Medicinal Chemistry s arguably the central journal in its field, the Journal of Medicinal Chemistry is a treasure trove of medicinal chemistry information. This information is still provided in a traditional print format, optimized over many years to be compact and yet easily understood by readers. Today, however, few readers have print subscriptions to the journal, and those of us with Web subscriptions rarely print out our electronic articles. Instead, we view them on computers and tablets, and these new media are creating exciting opportunities to innovate and enhance the value of our articles to readers. In addition, we are all benefiting from a Web of chemogenomics, systems biology, bioinformatics, and other Internet-based information resources that have sprung up in recent years. The value of the Journal of Medicinal Chemistry will be greatly enhanced if the data it contains can be thoughtfully integrated into this online data ecosystem. With this issue, therefore, the Journal of Medicinal Chemistry embarks on an initiative to integrate the chemical information it publishes with digital media and chemical software. The first step in this effort is the linkage of articles with molecular formulas in a format that can be generated by and read into chemical software. The immediate benefit is that readers will be able to transfer compounds from articles into chemical drawing programs, databases, and computational tools. In the near future, this association of articles with computer-readable chemical formulas will provide a foundation for the creation of new journal features that will bring chemistry to life on the Web and in digital readers and tablets. Authors are invited to use their existing chemical drawing programs (e.g., ChemDraw, ACD ChemSketch, Marvin Sketch) to generate a computer-readable SMILES formula1 for each compound presented in their articles. These formulas are then pasted into a simple spreadsheet, along with basic information about each compound. Ideally, this spreadsheet will provide a machine-readable version of the key data presented in the article’s tables. This approach, which balances functionality with ease of implementation and use, was developed by a committee comprising researchers and editors of the Journal of Medicinal Chemistry (Michael Gilson, Michael A. Walters, Patrick Walters, Carrie Haskell-Luevano, Gunda Georg, and Shaomeng Wang) and members of the ACS Publications Division and CAS (Janice Silverman and Kathy Wolfgram) in consultation with other individuals. It is worth noting that although InChi2 molecular formulas were seriously considered, the SMILES format was selected because its conventions allow it to preserve the author’s chemical drawings more faithfully. Incorporating computer-readable molecular formulas into Journal of Medicinal Chemistry articles is a simple yet powerful step toward making the journal even more relevant and useful in this digital age. Because the molecular formula spreadsheet makes the chemical information in an article so much more accessible, we expect it to raise the profile of articles that include it, and we hope that authors will find the process of filling out the molecular formula spreadsheet to be straightforward and worthwhile. In the coming year, we will work closely
A
© 2014 American Chemical Society
with ACS Publications staff to monitor the progress of this new initiative. We recognize that adjustments may be warranted and invite your comments and suggestions. Please send your comments to [email protected]. This issue’s Featured Article breaks ground for the Journal, as it is the first ever to include the new spreadsheet. All prospective authors are encouraged to follow suit, and all readers are invited to make use of the new data files. We hope that this initiative will stimulate other journals in the field to link their articles too, with compounds identifiers in the computer-readable SMILES format. This bridge between the written word and digital science has the potential to become a powerful tool in medicinal chemistry, chemical biology, and drug discovery.
Michael K. Gilson, Chair Molecular String Committee on Behalf of Journal of Medicinal Chemistry
Gunda Georg, Editor Journal of Medicinal Chemistry
Shaomeng Wang, Editor
■
Journal of Medicinal Chemistry
AUTHOR INFORMATION
Notes
The views expressed in this editorial are those of the author and not necessarily the views of the ACS.
■
REFERENCES
(1) Weininger, D. SMILES, a Chemical Language and InformationSystem. 1. Introduction to Methodology and Encoding Rules. J. Chem. Inf. Comput. Sci. 1988, 28, 31−36. (2) Stein, S. E.; Heller, S. R.; Tchekhovski, D. An Open Standard for Chemical Structure RepresentationThe IUPAC Chemical Identifier. Nimes Int. Chem. Inf. Conf. Proc. 2003, 143.
Published: February 12, 2014 1137
dx.doi.org/10.1021/jm5002056 | J. Med. Chem. 2014, 57, 1137−1137
